Fixed bug that would sometimes try to add an OXT to a non-protein residue

pdbfixer.py

@@ -60,6 +60,9 @@ substitutions = {
     'SEL':'SER', 'SEP':'SER', 'SET':'SER', 'SHC':'CYS', 'SHR':'LYS', 'SMC':'CYS', 'SOC':'CYS', 'STY':'TYR', 'SVA':'SER', 'TIH':'ALA',
     'SEL':'SER', 'SEP':'SER', 'SET':'SER', 'SHC':'CYS', 'SHR':'LYS', 'SMC':'CYS', 'SOC':'CYS', 'STY':'TYR', 'SVA':'SER', 'TIH':'ALA',
     'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
     'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
 }
 }
+proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
+rnaResidues = ['A', 'G', 'C', 'U']
+dnaResidues = ['DA', 'DG', 'DC', 'DT']
 
 
 def _overlayPoints(points1, points2):
 def _overlayPoints(points1, points2):
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
     """Given two sets of points, determine the translation and rotation that matches them as closely as possible.
@@ -192,7 +195,10 @@ class PDBFixer(object):
                         endPosition = startPosition+outward
                         endPosition = startPosition+outward
                         self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, residue, newAtoms, newPositions)
                         self._addMissingResiduesToChain(newChain, insertHere, startPosition, endPosition, residue, newAtoms, newPositions)
                         newResidue = list(newChain.residues())[-1]
                         newResidue = list(newChain.residues())[-1]
-                        terminalsToAdd = ['OXT']
+                        if newResidue.name in proteinResidues:
+                            terminalsToAdd = ['OXT']
+                        else:
+                            terminalsToAdd = None
                 
                 
                 # If a terminal OXT is missing, add it.
                 # If a terminal OXT is missing, add it.
                 
                 

ui.py

 import simtk.openmm.app as app
 import simtk.openmm.app as app
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
-from pdbfixer import PDBFixer, substitutions
+from pdbfixer import PDBFixer, substitutions, proteinResidues, dnaResidues, rnaResidues
 import uiserver
 import uiserver
 import webbrowser
 import webbrowser
 import os.path
 import os.path
 from cStringIO import StringIO
 from cStringIO import StringIO
 
 
-proteinResidues = ['ALA', 'ASN', 'CYS', 'GLU', 'HIS', 'LEU', 'MET', 'PRO', 'THR', 'TYR', 'ARG', 'ASP', 'GLN', 'GLY', 'ILE', 'LYS', 'PHE', 'SER', 'TRP', 'VAL']
-rnaResidues = ['A', 'G', 'C', 'U']
-dnaResidues = ['DA', 'DG', 'DC', 'DT']
-
 def loadHtmlFile(name):
 def loadHtmlFile(name):
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
     htmlPath = os.path.join(os.path.dirname(__file__), 'html')
     file = os.path.join(htmlPath, name)
     file = os.path.join(htmlPath, name)